Unfolding the mysteries of heterochromatin

Current Opinion in Genetics and Development

Volumn 8, Issue 2, 1998, Pages 147-153

  Wallrath, Lori L ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN STRUCTURE; CHROMOSOME; HETEROCHROMATIN; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; SILENCER GENE;

EID: 0032055402     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(98)80135-4     Document Type: Article

References (66)

1. Weiler KS, Wakimoto BT. Heterochromatin and gene expression in Drosophila. Annu Rev Genet. 29:1995;577-605.
2. Renauld H, Gasser SM. Heterochromatin: a meiotic matchmaker? Trends Cell Biol. 7:1997;201-205.
3. Grunstein M. Molecular model for telomeric heterochromatin in yeast. Curr Opin Cell Biol. 9:1997;383-387.
4. Allshire RC, Javerzat JP, Redhead NJ, Cranston G. Position effect variegation at fission yeast centromeres. Cell. 76:1994;157-169.
5. Nimmo ER, Cranston G, Allshire RC. Telomere-associated chromosome breakage in fission yeast results in variegated expression of adjacent genes. EMBO J. 13:1994;3801-3811.
6. Grewal SI, Klar AJ. Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis. Cell. 86:1996;95-101.
7. Festenstein R, Tolaini M, Corbella P, Mamalaki C, Parrington J, Fox M, Miliou A, Jones M, Kioussis D. Locus control region function and heterochromatin-induced position effect variegation. Science. 271:1996;1123-1125.
8. Milot E, Strouboulis J, Trimborn T, Wijgerde M, de Boer E, Langeveld A, Tan-Un K, Vergeer W, Yannoutsos N, Grosveld F, Fraser P. Heterochromatin effects on the frequency and duration of LCR-mediated gene transcription. Cell. 87:1996;105-114.
9. Marcand S, Gasser SM, Gilson E. Chromatin: a sticky silence. Curr Biol. 6:1996;1222-1225.
10. Marshall WF, Fung JC, Sedat JW. Deconstructing the nucleus: global architecture from local interactions. Curr Opin Genet Dev. 7:1997;259-263.
11. Riggs AD, Martienssen RA, Russo VEA. Introduction. Russo VEA, Martienssen RA, Riggs AD. Epigenetic Mechanisms of Gene Regulation. 1996;1-4 Cold Spring Harbor Laboratory Press, New York.
12. Belyaeva ES, Koryakov DE, Pokholkova GV, Demakova OV, Zhimulev IF. Cytological study of the brown dominant position effect. Chromosoma. 106:1997;124-132.
13. Wallrath LL, Elgin SCR. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 9:1995;1263-1277.
14. Lohe AR, Hilliker A, Roberts PA. Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics. 134:1993;1149-1174.
15. Fitzgerald DJ, Dryden GL, Bronson EC, Williams JS, Anderson JN. Conserved patterns of bending in satellite and nucleosome positioning DNA. J Biol Chem. 269:1994;21303-21314.
16. Widlund HR, Cao H, Simonsson S, Magnusson E, Simonsson T, Nielsen PE, Kahn JD, Crothers DM, Kubista M. Identification and characterization of genomic nucleosome-positioning sequences. J Mol Biol. 267:1997;807-817.
17. + allele at a homologous chromosomal location is also silenced. Examples of trans-silencing are also described in [22].
18. Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 10:1996;1796-1811.
19. Dernberg AF, Broman KW, Fung JC, Marshall WF, Philips J, Agard DA, Sedat JW. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell. 85:1996;745-759.
20. Csink AK, Henikoff S. Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature. 381:1996;529-531.
21. Henikoff S. Nuclear organization and gene expression: homologous pairing and long-range interactions. Curr Opin Cell Biol. 9:1997;388-395.
22. + transgenes and a neighboring vital gene at three different genomic locations. The data suggest that homology-dependent pairing is essential for trans-inactivation. The ability of a gene to be trans-inactivated may relate to its sensitivity to pairing disruptions.
23. Donaldson KM, Karpen GH. Trans-suppression of terminal deficiency-associated position effect variegation in a Drosophila minichromosome. Genetics. 145:1997;323-337.
24. Eberl DF, Lorenz LJ, Melnick MB, Sood V, Lasko P, Perrimon N. A new enhancer of position-effect variegation in Drosophila encodes a putative RNA helicase that binds chromosomes and is regulated by the cell cycle. of special interest Genetics. 146:1997;951-963 This paper describes the characterization of an essential gene, hel, that encodes an ATP-dependent RNA helicase (HEL). HEL is a haplo-enhancer and triplo-suppressor of PEV. HEL localizes to the nucleus of embryos in a cell cycle dependent fashion and is associated with larval salivary gland polytene chromosomes. Possible mechanisms for the regulation of chromatin formation by HEL are considered.
25. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 389:1997;349-352.
26. De Rubertis F, Kadosh D, Henchoz S, Pauli D, Reuter G, Struhl K, Spierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. of outstanding interest Nature. 384:1996;589-591 Cloning of E(var)364BC revealed a gene with similarity to the yeast transcriptional activator RPD3 and a human histone deacetylase. Mutations in RPD3 in yeast enhance telomeric PEV, suggesting a conservation of function through evolution. The authors hypothesize that RPD3 may serve to rapidly deacetylate newly deposited histones.
27. Fox CA, Ehrenhofer-Murray AE, Loo S, Rine J. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science. 276:1997;1547-1551.
28. Dillin A, Rine J. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics. 147:1997;1053-1062.
29. Pak DTS, Pflumm M, Chesnokov I, Huang DW, Kellum R, Marr J, Romanowski P, Botchan MR. The association of Drosophila origin recognition complex with heterochromatin and HP1. of outstanding interest Cell. 91:1997;311-323 This paper shows that the role of the ORC in silencing in S. cerevisiae is conserved in Drosophila. Co-immunoprecipition experiments and yeast two-hybrid screens demonstrate that ORC 1, 2, 5 and 6 interact with HP1 or HP1-containing complexes. The chromo domain and the chromo shadow domain are required for interactions. Evolutionary conservation of an interaction between ORC 1 and HP1 is demonstrated with Xenopus proteins. These data raise questions as to a possible link between DNA replication and chromatin folding.
30. Ehrenhofer-Murray AE, Gossen M, Pak DT, Botchan MR, Rine J. Separation of origin recognition complex functions by cross-species complementation. Science. 270:1995;1671-1674.
31. Granok H, Leibovitch BA, Shaffer CD, Elgin SCR. Ga-ga over GAGA factor. Curr Biol. 5:1995;238-241.
32. James TC, Eissenberg JC, Craig C, Dietrich V, Hobson A, Elgin SCR. Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur J Cell Biol. 50:1989;170-180.
33. Eissenberg JC, James TC, Foster-Hartnett DM, Hartnett T, Ngan V, Elgin SCR. Mutations in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci USA. 87:1990;9923-9927.
34. Singh PB, Miller JR, Pearce J, Kothary R, Burton RD, Paro R, James TC, Gaunt SJ. A sequence motif found in a Drosophila heterochromatin protein is conserved in animals and plants. Nucleic Acids Res. 19:1991;789-794.
35. Le Douarin B, Nielsen AL, Garnier J-M, Ichinose H, Jeanmougin F, Losson R, Chambon P. A possible involvement of TIFα and TIFβ in the epigenetic control of transcription by nuclear receptors. EMBO J. 15:1996;6701-6715.
36. Wreggett KA, Hill F, James PS, Hutchings A, Butcher GW, Singh PB. A mammalian homologue of Drosophila heterochromatin protein 1 (HP1) is a component of constitutive heterochromatin. Cytogenet Cell Genet. 66:1994;99-103.
37. Horsley D, Hutchings A, Butcher GW, Singh PB. M32, a murine homologue of Drosophila heterochromatin protein 1 (HP1), localises to euchromatin within interphase nuclei and is largely excluded from constitutive heterochromatin. Cytogenet Cell Genet. 73:1996;308-311.
38. Saunders WS, Chue C, Goebl M, Craig C, Clark RF, Powers JA, Eissenberg JC, Elgin SCR, Rothfield NF, Earnshaw WC. Molecular cloning of a human homologue of Drosophila heterochromatin protein HP1 using anti-centromere autoantibodies with antichromo specificity. J Cell Sci. 104:1993;573-582.
39. Nicol L, Jeppesen P. Human autoimmune sera recognize a conserved 26 kD protein associated with mammalian heterochromatin that is homologous to heterochromatin protein 1 of Drosophila. Chromosome Res. 2:1994;245-253.
40. Ye Q, Worman HJ. Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1. J Biol Chem. 271:1996;14653-14656.
41. HSβ (p25β) and its localization with centromeres in mitosis. Chromosoma. 106:1997;11-19.
42. Koonin EV, Zhou S, Lucchesi JC. The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 23:1995;4229-4233.
43. Ball LJ, Murzina NV, Broadhurst RW, Raine ARC, Archer SJ, Stott FJ, Murzin AG, Singh PB, Domaille PJ, Laue ED. Structure of the chromatin binding (chromo) domain from mouse modifier protein 1. EMBO J. 16:1997;2473-2481.
44. Paro R, Hogness D. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci USA. 88:1992;263-267.
45. Aasland R, Stewart AF. The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1. Nucleic Acids Res. 23:1995;3168-3173.
46. Powers JA, Eissenberg JC. Overlapping domains of the heterochromatin-associated protein HP1 mediate nuclear localization and heterochromatin binding. J Cell Biol. 120:1993;291-299.
47. Cléard F, Delattre M, Spierer P. SU(VAR)3-7, a Drosophila heterochromatin-associated protein and companion of HP1 in the genomic silencing of position-effect variegation. of outstanding interest EMBO J. 16:1997;5280-5288 Su(var)3-7 is a haplo-suppressor and a triplo-enhancer of PEV. SU(VAR)3-7 and HP1 co-localize to heterochromatin in the early embryo; the data suggest a cell cycle dependent association with chromosomes. SU(VAR)3-7 and HP1 co-localize on larval polytene chromosomes, including sites on the small, mostly heterochromatic fourth chromosome. A biochemical demonstration of physical interactions is demonstrated.
48. Frankel S, Sigel EA, Craig C, Elgin SCR, Mooseker MS, Artavanis-Tsakonas S. An actin-related protein in Drosophila colocalizes with heterochromatin protein 1 in pericentric heterochromatin. of special interest J Cell Sci. 110:1997;1999-2012 Arp4, an actin-related protein, and HP1 co-localize in the early embryo and larval mitotic cells. On larval polytene chromosome, Arp4 and HP1 co-localize to pericentric heterochromatin but they have distinct localization patterns in euchromatin. A swap of the chromo domain in HP1 for that of Polycomb causes mislocation of the chimeric HP1, endogenous HP1 and Arp4 to Polycomb-binding sites.
49. Reifsnyder C, Lowell J, Clarke A, Pillus L. Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat Genet. 14:1996;42-49.
50. Ehrenhofer-Murray AE, Rivier DH, Rine J. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics. 145:1997;923-934.
51. Baricheva EA, Berrios M, Bogachev SS, Borisevich IV, Lapik ER, Sharakhov IV, Stuurman N, Fisher PA. DNA from Drosophila melanogaster β-heterochromatin binds specifically to nuclear lamins in vitro and the nuclear envelope in situ. Gene. 171:1996;171-179.
52. Reuter G, Giarre M, Farah J, Gausz J, Spierer A, Spierer P. Dependence of position-effect variegation in Drosophila on dose of a gene encoding an unusual zinc-finger protein. Nature. 344:1990;219-223.
53. Tschiersch B, Hofmann A, Krauss V, Dom R, Korge G, Reuter G. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13:1994;3822-3831.
54. Baska K, Morawietz H, Dombrádi V, Axton M, Taubert H, Szabó G, Török I, Udvardy A, Gyurkovics H, Szöör B, et al. Mutations in the protein phosphatase 1 gene at 87B can differentially affect suppression of position-effect variegation and mitosis in Drosophila melanogaster. Genetics. 135:1993;117-125.
55. Garzino V, Pereira A, Laurenti P, Graba Y, Levis RW, Le Parco Y, Pradel J. Cell lineage-specific expression of modulo, a dose-dependent modifier of variegation in Drosophila. EMBO J. 11:1992;4471-4479.
56. Larsson J, Zhang J, Rasmuson-Lestander Å. Mutations in the Drosophila melanogaster gene encoding S-adensylmethionine suppress position-effect variegation. Genetics. 143:1996;887-896.
57. Csink AK, Linsk R, Birchler JA. The Lighten up (Lip) gene of Drosophila melanogaster, a modifier of retroelement expression, position effect variegation and white locus insertion alleles. Genetics. 138:1994;153-163.
58. Birchler JA, Bhadra U, Rabinow L, Linsk R, Nguyen-Huyuh AT. Weakener of white (Wow), a gene that modifies the expression of the white eye color locus and that suppresses position effect variegation in Drosophila melanogaster. Genetics. 137:1994;1057-1070.
59. Bhadra U, Birchler JA. Characterization of a sex-influenced modifier of gene expression and suppressor of position-effect variegation in Drosophila. Mol Gen Genet. 250:1996;601-613.
60. Henderson DS, Banga SS, Grigliatti TA, Boyd JB. Mutagen sensitivity and suppression of position-effect variegation result from mutations in mus209, the Drosophila gene encoding PCNA. EMBO J. 13:1994;1450-1459.
61. Gerasimova TI, Gdula DA, Gerasimov DV, Simonova O, Corces VG. A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell. 82:1995;587-597.
62. Seum C, Spierer A, Pauli D, Szidonya J, Reuter G, Spierer P. Position-effect variegation in Drosophila depends on the dose of the gene encoding the E2F transcriptional activator and cell cycle regulator. Development. 122:1996;1949-1956.
63. Henchoz S, De Rubertis F, Pauli D, Spierer P. The dose of a putative ubiquitin-specific protease affects position-effect variegation in Drosophila melanogaster. Mol Cell Biol. 16:1996;5717-5725.
64. Judd BH. Mutations of zeste that mediate transvection are recessive enhancers of position-effect variegation in Drosophila melanogaster. Genetics. 141:1995;245-253.
65. Frolov MV, Benevolenskaya EV, Birchler JA. Regena (Rga), a Drosophila homolog of the global negative transcriptional regulator CDC36 (NOT2) from yeast, modifier gene expression and suppresses position effect variegation. Genetics. 148:1998;317-329.
66. Sinclair DAR, Clegg NJ, Antonchuk A, Milne TA, Stankunas K, Ruse C, Grigliatti TA, Kassis JA, Brock HW. Enhancer of Polycomb is a suppressor of position-effect variegation in Drosophila melanogaster. Genetics. 148:1998;211-220.